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New resources and strategies for genome-wide mapping in sorghum

New resources and strategies for genome-wide mapping in sorghum. Geoff Morris Research Assistant Professor Kresovich Lab University of South Carolina. Why do we need gene-resolution mapping (or causal variants)?.

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New resources and strategies for genome-wide mapping in sorghum

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  1. New resources and strategies for genome-wide mapping in sorghum Geoff Morris Research Assistant Professor Kresovich Lab University of South Carolina

  2. Why do we need gene-resolution mapping (or causal variants)? • More accurate marker-assisted selection, in breeding programs and from germplasm • Leverage knowledge from other crops and model plant species

  3. Genotyping-by-sequencing identified 265,000 SNP markers

  4. An atlas of genomic variation in 1000 sorghum accessions Genetic Variation: Recombination rates:

  5. Mapping genes underlying traitvariation using genome-wide association studies (GWAS) Linked SNP G G G C C C Phenotype Tallest Taller Tall Short Shorter Shortest Causative A A A T T T Unlinked SNP G C G C G G * Height G C A T G C p= 10-0 p < 10-8 Quantitative trait locus(Candidate gene)

  6. DFL2 LOM3 GWAS reveals multiple loci controlling panicle branch length THE1 LUG ID1 TCP,TLK APO1 GDD1 SP1 BDE1,ID1 CLV1 ID1 Thick tassel dwarf1 homolog Short panicle1 homolog Aberrant panicle organization1 ortholog Peptide transporter in rice (Li et al. 2009 Plant J) Receptor-like kinase in maize (Lunde and Hake 2009 Genetics) F-box protein in rice (Ikeda et al. 2005 DevBiol)

  7. Back to basics: Pigmentation

  8. Testing GWAS with validated flavonoid genes • The classical testa gene B2was cloned as Tannin1 • G/T polymorphism found in GBS data • Positive control for GWAS in sorghum Wu et al. PNAS 2012

  9. Mapping testa (presence/absence) in an association panel • GLM and CMLM (K, Q+K) identify the locus but not the gene

  10. Synthetic associations can prevent gene-level resolution in GWAS MAF=46% Synthetic associations tan1-a allele MAF=20% Caused by multiple independent mutations in the same gene: Orozco et al. 2010

  11. Gene-resolution mapping of Tannin1 • GLM (Q) and MLM (K) do map Tannin1 precisely

  12. Precise mapping of Tannin1 in recombinant inbred lines • One day of scratch tests + GBS data = Precise mapping of Tannin1 Stem borer mapping population (n=263)

  13. Pericarp pigmentation in the sorghum association panel Ibraheem et al. 2010 Yellow seed1 cloned by Chopra lab

  14. Basal seedling (coleoptile) pigmentation mapped in a RIL Arabidopsis TT8 Maize B1

  15. Adult plant pigmentation (tan vs. purple) mapped in a RIL • Colocalizes with classical P locus • Maps to cluster of DFR (Maize A1)

  16. Lessons learned • Higher-density genotyping will yield more useful mapping results • Genotyping-by-sequencing gets the most out of existing investments in RILs • GWAS can provide gene-resolution mapping but signals may be complex/indirect • Best of both worlds: • Nested Association Mapping (NAM) • Regional Mapping (RegMap)

  17. Mapping climate-associated alleles in a high-resolution global diversity panel • 700,000 SNPs genotyped in 2,500 source-identified accessions of African and Asian origin

  18. Starting November 1 Assistant Professor Sorghum Genetics and Genomics Department of Agronomy More info: www.morrislab.org

  19. Project team University of South Carolina Stephen Kresovich, Davina Rhodes, Zachary Brenton Cornell University/Institute for Genomic Diversity/USDA-ARS SNP pipeline: Ed Buckler, Jeff Glaubitz, James Harriman Genotyping: Sharon Mitchell, Charlotte Acharya International Crops Research Institute for the Semi-Arid Tropics (ICRISAT – Patancheru, India) PunnaRamu* Germplasm: Tom Hash, Oscar Riera-Lizarazu, HariUpadhyaya, SantoshDeshpande, VinayanMadhumal Bioinformatics: Trushar Shah University of Illinois Phenotypes: Patrick Brown Iowa State University Jianming Yu Funding NSF/Gates-Basic Research to Enable Agricultural Development USDA-Feedstock Genomics

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